feat: 接入 Pi 内置 codemode，并修复全面审查发现的问题

- codemode：Tool Search 常驻（alwaysEnabled）、权限 allow（嵌套调用仍逐个过权限门）、
  tools.jsonc 登记使用规则；RTK 跳过 parentToolCallId 嵌套调用，避免丢失 bash
  structuredContent；Tool Search 目录过滤 hidden / codemode（script-only）exposure；
  扩展加载测试加载 builtin:codemode 并断言其常驻激活
- 搜索 key 不再经命令行参数传递：search-auth.mjs 改为 --set-stdin（先读校验再加锁），
  configure.sh 交互输入经管道、非交互用 --<provider> -
- CodeGraph 客户端监听子进程 stdin error，避免 EPIPE 未处理导致崩溃
- 移除 PI_TOOL_SEARCH/HERMES_MEMORY/RTK_CONFIG_PATH 环境变量入口，测试改用工厂 configPath 注入
- pi-subagents 固定 vitest / coverage-istanbul 4.1.10，修复 npm ls 版本冲突
- 补 pi-web-search / pi-worktree UPSTREAM.md 与 pi-minimal-footer AGENTS.md，
  files 白名单补齐并加测试；.codegraph/.gitignore 移出跟踪
- detect_kitty 优先识别官方安装目录

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pi-web-search/README.md

@@ -30,7 +30,10 @@ Keys live in Pi's `auth.json` as one `api_key` credential per provider
 (`tavily`, `exa`, `keenable`), read by `auth.ts` with upstream resolution
 semantics — literal values, `$VAR`/`${VAR}` interpolation, and `!command`
 indirection (e.g. `"!op read op://Vault/Tavily/key"`). `configure.sh search`
-writes them (atomically, mode 600, preserving all other entries); process
+writes them via its hidden interactive prompt or `scripts/search-auth.mjs
+--set-stdin` reading the key from stdin — a key is never accepted as a
+command-line argument (atomically, mode 600, preserving all other entries);
+process
 environment variables are not read directly — use `"key": "$TAVILY_API_KEY"`
 to indirect through env. `KEENABLE_API_URL` stays env-only, or can be stored
 in the keenable credential's `env` map.